A non-federated Portal for ArcGIS 10.3 web map does not send a returnGeometry query request when adding an ArcGIS Server 10.3 Map Service layer from the web (/MapServer/#) upon the first attempt when this server service is being accessed via the web adaptor and web tier security is configured on the ArcGIS Server site, but not applied to the service.
1) Add the map service layer twice, however this stores two copies in the map details.
2) Work from the entire map service rather than the particular layers.